Abstract
Alternative splicing (AS) increases the diversity of transcripts and proteins through the selection of different splice sites and plays an important role in the growth, development and stress tolerance of plants. With the release of the reference genome of the tea plant (Camellia sinensis) and the development of transcriptome sequencing, researchers have reported the existence of AS in tea plants. However, there is a lack of a platform, centered on different RNA-seq datasets, that provides comprehensive information on AS.To facilitate access to information on AS and reveal the molecular function of AS in tea plants, we established the first comprehensive AS database for tea plants (TeaAS, http://www.teaas.cn/index.php). In this study, 3.96 Tb reads from 66 different RNA-seq datasets were collected to identify AS events. TeaAS supports four methods of retrieval of AS information based on gene ID, gene name, annotation (non-redundant/Kyoto encyclopedia of genes and genomes/gene ontology annotation or chromosomal location) and RNA-seq data. It integrates data pertaining to genome annotation, type of AS event, transcript sequence, and isoforms expression levels from 66 RNA-seq datasets. The AS events resulting from different environmental conditions and that occurring in varied tissue types, and the expression levels of specific transcripts can be clearly identified through this online database. Moreover, it also provides two useful tools, Basic Local Alignment Search Tool and Generic Genome Browser, for sequence alignment and visualization of gene structure.The features of the TeaAS database make it a comprehensive AS bioinformatics platform for researchers, as well as a reference for studying AS events in woody crops. It could also be helpful for revealing the novel biological functions of AS in gene regulation in tea plants.
Highlights
Alternative splicing (AS) refers to pre-mRNA processing events that produce multiple mRNAs from the same gene through variable selection of splice sites
The gene involved in the AS of an MYB transcription factor affects anthocyanin biosynthesis in tomato fruits, and mutations in the splice sites cause a complete loss of function in the wild-type protein [6]
A comprehensive AS database of plant communities was established, including that of cotton [11], tomato [12], fruit plants [13], Brachypodium distachyon [14] and other crops. The establishment of these databases enriches the knowledge on gene functions and facilitates access to AS-related information; till date, there is no comprehensive database of AS in tea plants (Camellia sinensis)
Summary
Alternative splicing (AS) refers to pre-mRNA processing events that produce multiple mRNAs from the same gene through variable selection of splice sites. The results showed that a total of 131,924 AS events were identified in 11,320 genes in the transcriptome of PRJNA576575, whereas only 9,152 AS events were identified in a self-incompatibility transcriptome (PRJNA355226) This may be due to the differences in treatment conditions of the tea plants and the size of the sequencing data. A search with the ID CSS0005154.1 yields the result that the gene encodes a NAC transcription factor and undergoes AS events under multiple treatment conditions, such as salt stress, exposure to sucrose, and cold acclimation. A 30 bp nucleic acid sequence was lacking in the AS isoform, this sequence was not present in the WRKY domain (Fig. 4e)
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